FMO DATABASE

FMODB ID: 66KYZ

Calculation Name: 2YV4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YV4

Chain ID: A

ChEMBL ID:

UniProt ID: O73972

Base Structure: X-ray

Registration Date: 2023-06-19

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	105
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-792553.265627
FMO2-HF: Nuclear repulsion	752870.948747
FMO2-HF: Total energy	-39682.31688
FMO2-MP2: Total energy	-39799.715227

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:236:ALA)

Summations of interaction energy for fragment #1(A:236:ALA)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-7.975	-5.765	0.062	-0.979	-1.293	0.003

Interaction energy analysis for fragmet #1(A:236:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.035 / q_NPA : -0.025

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	238	ASN	0	-0.039	-0.033	3.826	-0.659	1.003	-0.015	-0.795	-0.853	0.003
4	A	239	ALA	0	0.013	0.028	6.265	0.607	0.607	0.000	0.000	0.000	0.000
5	A	240	GLU	-1	-0.955	-0.970	7.300	-0.706	-0.706	0.000	0.000	0.000	0.000
6	A	241	VAL	0	0.003	-0.002	6.466	0.074	0.074	0.000	0.000	0.000	0.000
7	A	242	ILE	0	-0.011	-0.009	9.419	0.179	0.179	0.000	0.000	0.000	0.000
8	A	243	VAL	0	0.006	0.008	11.758	-0.016	-0.016	0.000	0.000	0.000	0.000
9	A	244	VAL	0	-0.019	-0.003	14.234	0.019	0.019	0.000	0.000	0.000	0.000
10	A	245	GLU	-1	-0.906	-0.963	18.009	0.110	0.110	0.000	0.000	0.000	0.000
11	A	246	GLY	0	0.028	0.012	19.998	-0.012	-0.012	0.000	0.000	0.000	0.000
12	A	247	PRO	0	0.011	0.014	23.687	-0.001	-0.001	0.000	0.000	0.000	0.000
13	A	248	ARG	1	1.002	0.970	24.837	-0.011	-0.011	0.000	0.000	0.000	0.000
14	A	249	GLU	-1	-0.971	-0.975	25.905	-0.035	-0.035	0.000	0.000	0.000	0.000
15	A	250	LYS	1	0.977	0.978	26.749	-0.002	-0.002	0.000	0.000	0.000	0.000
16	A	251	VAL	0	-0.005	0.005	20.961	-0.013	-0.013	0.000	0.000	0.000	0.000
17	A	252	LYS	1	0.829	0.899	23.215	0.063	0.063	0.000	0.000	0.000	0.000
18	A	253	GLY	0	0.015	0.027	24.988	-0.017	-0.017	0.000	0.000	0.000	0.000
19	A	254	LYS	1	0.873	0.940	21.737	0.079	0.079	0.000	0.000	0.000	0.000
20	A	255	ILE	0	0.011	0.005	19.185	-0.018	-0.018	0.000	0.000	0.000	0.000
21	A	256	THR	0	-0.027	-0.035	21.697	-0.025	-0.025	0.000	0.000	0.000	0.000
22	A	257	GLU	-1	-0.920	-0.950	24.619	-0.121	-0.121	0.000	0.000	0.000	0.000
23	A	258	LEU	0	0.025	0.003	18.523	-0.011	-0.011	0.000	0.000	0.000	0.000
24	A	259	VAL	0	0.004	0.018	19.874	-0.030	-0.030	0.000	0.000	0.000	0.000
25	A	260	LYS	1	0.932	0.967	21.586	0.127	0.127	0.000	0.000	0.000	0.000
26	A	261	GLU	-1	-0.877	-0.941	22.992	-0.173	-0.173	0.000	0.000	0.000	0.000
27	A	262	LEU	0	-0.074	-0.052	17.090	-0.013	-0.013	0.000	0.000	0.000	0.000
28	A	263	LYS	1	0.923	0.962	21.023	0.255	0.255	0.000	0.000	0.000	0.000
29	A	264	GLU	-1	-0.960	-0.961	23.103	-0.195	-0.195	0.000	0.000	0.000	0.000
30	A	265	ARG	1	0.882	0.941	18.500	0.290	0.290	0.000	0.000	0.000	0.000
31	A	266	GLY	0	-0.015	-0.006	22.444	-0.009	-0.009	0.000	0.000	0.000	0.000
32	A	267	LYS	1	0.841	0.935	16.106	0.443	0.443	0.000	0.000	0.000	0.000
33	A	268	LYS	1	0.933	0.974	16.950	0.635	0.635	0.000	0.000	0.000	0.000
34	A	269	VAL	0	-0.009	-0.022	16.123	-0.080	-0.080	0.000	0.000	0.000	0.000
35	A	270	GLY	0	0.040	0.007	14.936	0.034	0.034	0.000	0.000	0.000	0.000
36	A	271	VAL	0	-0.026	-0.007	15.066	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	272	ILE	0	-0.020	-0.008	10.743	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	273	GLY	0	0.030	-0.018	15.162	0.046	0.046	0.000	0.000	0.000	0.000
39	A	274	SER	0	-0.096	-0.076	18.282	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	275	GLU	-1	-0.835	-0.901	21.602	-0.102	-0.102	0.000	0.000	0.000	0.000
41	A	276	SER	0	0.042	0.017	21.045	-0.009	-0.009	0.000	0.000	0.000	0.000
42	A	277	TYR	0	0.028	0.003	20.866	-0.009	-0.009	0.000	0.000	0.000	0.000
43	A	278	ASN	0	-0.053	-0.038	23.976	-0.012	-0.012	0.000	0.000	0.000	0.000
44	A	279	ALA	0	-0.020	-0.001	18.993	-0.003	-0.003	0.000	0.000	0.000	0.000
45	A	280	ASP	-1	-0.858	-0.926	19.184	-0.370	-0.370	0.000	0.000	0.000	0.000
46	A	281	GLU	-1	-0.891	-0.954	16.407	-0.525	-0.525	0.000	0.000	0.000	0.000
47	A	282	PHE	0	-0.028	-0.021	17.708	0.012	0.012	0.000	0.000	0.000	0.000
48	A	283	PHE	0	-0.013	-0.006	14.430	-0.013	-0.013	0.000	0.000	0.000	0.000
49	A	284	PHE	0	-0.002	0.011	16.515	0.016	0.016	0.000	0.000	0.000	0.000
50	A	285	LEU	0	-0.004	0.003	14.459	-0.003	-0.003	0.000	0.000	0.000	0.000
51	A	286	GLY	0	0.036	0.010	16.393	0.039	0.039	0.000	0.000	0.000	0.000
52	A	287	SER	0	-0.087	-0.033	19.130	0.001	0.001	0.000	0.000	0.000	0.000
53	A	288	SER	0	0.027	0.004	20.749	0.016	0.016	0.000	0.000	0.000	0.000
54	A	289	VAL	0	0.069	0.023	18.512	0.002	0.002	0.000	0.000	0.000	0.000
55	A	290	GLU	-1	-0.937	-0.967	17.693	0.197	0.197	0.000	0.000	0.000	0.000
56	A	291	GLU	-1	-0.890	-0.961	17.390	0.042	0.042	0.000	0.000	0.000	0.000
57	A	292	VAL	0	0.011	0.025	14.073	-0.009	-0.009	0.000	0.000	0.000	0.000
58	A	293	ALA	0	-0.032	-0.024	13.118	0.019	0.019	0.000	0.000	0.000	0.000
59	A	294	LYS	1	0.926	0.974	12.413	-0.006	-0.006	0.000	0.000	0.000	0.000
60	A	295	ASN	0	-0.031	-0.026	12.959	-0.026	-0.026	0.000	0.000	0.000	0.000
61	A	296	LEU	0	0.042	0.038	8.775	-0.103	-0.103	0.000	0.000	0.000	0.000
62	A	297	PHE	0	0.025	-0.009	4.962	-0.324	-0.324	0.000	0.000	0.000	0.000
63	A	298	LYS	1	0.899	0.953	7.396	-0.094	-0.094	0.000	0.000	0.000	0.000
64	A	299	ALA	0	0.023	0.015	10.034	-0.139	-0.139	0.000	0.000	0.000	0.000
65	A	300	LEU	0	0.035	0.001	5.512	-0.016	-0.016	0.000	0.000	0.000	0.000
66	A	301	ARG	1	0.939	0.984	6.151	0.146	0.146	0.000	0.000	0.000	0.000
67	A	302	TYR	0	-0.072	-0.022	7.900	0.012	0.012	0.000	0.000	0.000	0.000
68	A	303	MET	0	0.001	0.006	9.922	0.051	0.051	0.000	0.000	0.000	0.000
69	A	304	ASP	-1	-0.750	-0.861	6.257	-3.928	-3.928	0.000	0.000	0.000	0.000
70	A	305	LYS	1	0.880	0.951	9.738	0.837	0.837	0.000	0.000	0.000	0.000
71	A	306	ALA	0	-0.026	-0.013	12.235	0.130	0.130	0.000	0.000	0.000	0.000
72	A	307	GLY	0	-0.015	-0.005	13.046	0.125	0.125	0.000	0.000	0.000	0.000
73	A	308	VAL	0	-0.061	-0.023	12.681	0.095	0.095	0.000	0.000	0.000	0.000
74	A	309	ASP	-1	-0.819	-0.890	12.058	-0.897	-0.897	0.000	0.000	0.000	0.000
75	A	310	VAL	0	-0.052	-0.032	11.913	-0.086	-0.086	0.000	0.000	0.000	0.000
76	A	311	VAL	0	0.024	0.004	9.738	0.051	0.051	0.000	0.000	0.000	0.000
77	A	312	ILE	0	0.001	-0.002	11.945	0.058	0.058	0.000	0.000	0.000	0.000
78	A	313	ALA	0	-0.032	-0.023	11.751	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	314	GLU	-1	-0.777	-0.864	13.849	-0.051	-0.051	0.000	0.000	0.000	0.000
80	A	315	GLY	0	0.004	-0.011	16.968	0.029	0.029	0.000	0.000	0.000	0.000
81	A	316	VAL	0	-0.019	-0.006	17.940	0.008	0.008	0.000	0.000	0.000	0.000
82	A	317	GLU	-1	-0.893	-0.950	21.405	0.078	0.078	0.000	0.000	0.000	0.000
83	A	318	GLU	-1	-0.843	-0.930	23.679	0.039	0.039	0.000	0.000	0.000	0.000
84	A	319	ARG	1	0.904	0.933	23.872	-0.041	-0.041	0.000	0.000	0.000	0.000
85	A	320	GLY	0	0.057	0.037	22.240	0.012	0.012	0.000	0.000	0.000	0.000
86	A	321	LEU	0	-0.031	-0.006	19.076	0.030	0.030	0.000	0.000	0.000	0.000
87	A	322	GLY	0	0.078	0.037	17.286	0.021	0.021	0.000	0.000	0.000	0.000
88	A	323	LEU	0	0.006	0.019	16.272	0.029	0.029	0.000	0.000	0.000	0.000
89	A	324	ALA	0	-0.020	-0.008	16.038	0.069	0.069	0.000	0.000	0.000	0.000
90	A	325	VAL	0	-0.005	-0.004	11.980	0.094	0.094	0.000	0.000	0.000	0.000
91	A	326	MET	0	0.019	0.012	11.551	0.095	0.095	0.000	0.000	0.000	0.000
92	A	327	ASN	0	-0.002	0.000	11.754	0.168	0.168	0.000	0.000	0.000	0.000
93	A	328	ARG	1	0.862	0.943	8.732	-0.732	-0.732	0.000	0.000	0.000	0.000
94	A	329	LEU	0	0.011	-0.008	6.644	0.370	0.370	0.000	0.000	0.000	0.000
95	A	330	ARG	1	0.833	0.935	5.567	-3.289	-3.289	0.000	0.000	0.000	0.000
96	A	331	LYS	1	1.026	1.013	9.605	-1.025	-1.025	0.000	0.000	0.000	0.000
97	A	332	ALA	0	-0.031	-0.036	7.232	0.347	0.347	0.000	0.000	0.000	0.000
98	A	333	SER	0	-0.001	-0.007	3.204	0.644	1.182	0.078	-0.178	-0.438	0.000
99	A	334	GLY	0	0.023	0.022	4.817	-0.775	-0.765	-0.001	-0.006	-0.002	0.000
100	A	335	TYR	0	0.003	0.009	7.049	-0.295	-0.295	0.000	0.000	0.000	0.000
101	A	336	LYS	1	0.978	1.002	9.587	0.264	0.264	0.000	0.000	0.000	0.000
102	A	337	ILE	0	0.033	0.018	13.266	-0.011	-0.011	0.000	0.000	0.000	0.000
103	A	338	VAL	0	-0.037	-0.022	15.899	-0.008	-0.008	0.000	0.000	0.000	0.000
104	A	339	LYS	1	1.001	1.010	18.972	-0.018	-0.018	0.000	0.000	0.000	0.000
105	A	340	ALA	0	-0.031	-0.021	22.102	-0.009	-0.009	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:236:ALA)